Same directory structures
You have the MOS: assign and stuff, it might be confusing where put libraries.
UI is even more configurable because it's MUI
So if you don't like MUI, original AmigaOS 3.x uses Gadtools.
AmigaOS3.5/3.9 uses reaction.
Some who has only used a Amiga 500 / Workbench 1.2 will most likely not know what MUI is.
MUI, TurboPrint, SFS, CGX, Poseidon
None of this are bundled with AmigaOS 3.x, most people don't have USB on classic Amiga, and True colors, sure some one who has spent a lot of money on upgrades maybe.
AHI
Became a part of AmigaOS 3.5/3.9, it was not part of AmigaOS 3.1, some one who has not used Amiga in few years might find it strange to configure.
Ambient is MUCH more configurable than WB ever was
Some people like Dopus5 and some don't, this is about individual taste, we do not all like the same thing, for the most part I like to use workbench because I feel I have better control when dragging icons around. Besides I see all buttons as clutter on the screen, when just want to start and find some thing.
probably any other system (including real Amigas).
How well does it support OCS/AGA games :-)